There is nothing wrong with putting on a new saddle and clipless pedals. Just keep the old ones. The only vintage saddles that are worth riding are Brooks, but they don't really go with vintage Italian any better than a new saddle, in my opinion.
The neck and wrist pain would indicate the bars are too low. If you are maxed out on stem height, you can get a Nitto Technomic stem from Harris Cyclery that wouldn't hurt the vintage look, but allow you to get the bars a lot higher than a typical stem.
Remember, it is better to have a bike that you can ride than a bike that looks original. Nobody can see the saddle and pedals when you are riding it, anyway. You can always replace everything when you sell it. In fact, I have never sold a bike with the pedals and saddle I actually used.